I think the playoff system works perfectly as is right now, unless the NFL adds more teams there's no real reason to change it.
The only way I could accept changing to allow the teams with the best record to have a bye it is if they were to eliminate the AFC and NFC completely - otherwise how can you justify giving Philadelphia (the 4th best team in the NFC by record) a home game whilst forcing one of the 3 11-5 AFC teams to go on the road, or keep Arizona at home with a 10-6 record but allow San Diego into the playoffs as a wildcard with 1 less win. Winning your division should always qualify you for the playoffs at an absolute minimum. Then, in a tiebreaker between two teams with equal record, you could have divisional standing is the first tiebreaker instead of H2H, so at least there's still SOME value to winning your division (ie. New England would still have the tiebreak over SF)
Then you have a best of 12 seeding, and the 2013 season playoffs would look something like:
BYES: Seattle (1), Denver (2), Carolina (3), New England (4) (this might not be accurate, I haven't bothered to check record against common opponents or strength of schedule)
Home game in WC round:
SF (5), Cincinatti (6), Indianapolis (7), New Orleans(8)
Road game in WC round:
Kansas City (9), Philadelphia (10), Arizona Cardinals (11), Green Bay (12)
I do like the fact that the Superbowl will always be between an AFC and NFC champion - but at the same time, the Superbowl should be between the best 2 teams in teh league, not the best 2 teams from each conference.